data_5JAX # _model_server_result.job_id tcRuMAaotgaRoH2wNid02w _model_server_result.datetime_utc '2024-10-12 18:15:34' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5jax # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5JAX # _exptl.entry_id 5JAX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 424.101 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-8-bromo-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-1,9-dihydro-6H-purin-6-one _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5JAX _cell.length_a 47.01 _cell.length_b 47.01 _cell.length_c 102.59 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JAX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD2 ASP 55 A ASP 271 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc2 A O LYS 92 A LYS 308 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc3 A O GLN 95 A GLN 311 1_555 E NA NA . A NA 404 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc4 A O GLU 97 A GLU 313 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc5 A OD2 ASP 98 A ASP 314 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc6 A O GLY 126 A GLY 342 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc7 A OD1 ASP 128 A ASP 344 1_555 C CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.926 ? metalc ? metalc8 C CA CA . A CA 402 1_555 F O HOH . A HOH 516 6_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc9 C CA CA . A CA 402 1_555 F O HOH . A HOH 573 6_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc10 C CA CA . A CA 402 1_555 F O HOH . A HOH 606 6_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc11 E NA NA . A NA 404 1_555 F O HOH . A HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc12 E NA NA . A NA 404 1_555 F O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc13 E NA NA . A NA 404 1_555 F O HOH . A HOH 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? # _chem_comp.formula 'C10 H11 Br N5 O7 P' _chem_comp.formula_weight 424.101 _chem_comp.id 6J7 _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-8-bromo-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-1,9-dihydro-6H-purin-6-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O P 6J7 doub 1 n n O2 P 6J7 sing 2 n n N2 C6 6J7 sing 3 n n P O3 6J7 sing 4 n n P O1 6J7 sing 5 n n O3 C1 6J7 sing 6 n n C6 N3 6J7 sing 7 n n C6 N1 6J7 doub 8 n n O1 C 6J7 sing 9 n n N3 C7 6J7 sing 10 n n C1 C2 6J7 sing 11 n n C1 C3 6J7 sing 12 n n N1 C5 6J7 sing 13 n n C C3 6J7 sing 14 n n C2 O4 6J7 sing 15 n n C2 C4 6J7 sing 16 n n C3 O5 6J7 sing 17 n n C7 O6 6J7 doub 18 n n C7 C8 6J7 sing 19 n n C5 C8 6J7 doub 20 n y C5 N 6J7 sing 21 n y O5 C4 6J7 sing 22 n n C8 N4 6J7 sing 23 n y C4 N 6J7 sing 24 n n N C9 6J7 sing 25 n y N4 C9 6J7 doub 26 n y C9 BR 6J7 sing 27 n n N3 H10 6J7 sing 28 n n N2 H8 6J7 sing 29 n n N2 H9 6J7 sing 30 n n C4 H7 6J7 sing 31 n n C2 H3 6J7 sing 32 n n O4 HO4 6J7 sing 33 n n C3 H6 6J7 sing 34 n n C H1 6J7 sing 35 n n C H 6J7 sing 36 n n C1 H5 6J7 sing 37 n n O2 H2 6J7 sing 38 n n # _atom_sites.entry_id 5JAX _atom_sites.fract_transf_matrix[1][1] 0.021272 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021272 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009748 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 6J7 A 1 401 3 6J7 8br . C 3 CA A 1 402 2 CA CA . D 3 CA A 1 403 3 CA CA . E 4 NA A 1 404 1 NA NA . F 5 HOH A 1 501 107 HOH HOH . F 5 HOH A 2 502 127 HOH HOH . F 5 HOH A 3 503 18 HOH HOH . F 5 HOH A 4 504 82 HOH HOH . F 5 HOH A 5 505 17 HOH HOH . F 5 HOH A 6 506 13 HOH HOH . F 5 HOH A 7 507 120 HOH HOH . F 5 HOH A 8 508 116 HOH HOH . F 5 HOH A 9 509 59 HOH HOH . F 5 HOH A 10 510 66 HOH HOH . F 5 HOH A 11 511 63 HOH HOH . F 5 HOH A 12 512 85 HOH HOH . F 5 HOH A 13 513 40 HOH HOH . F 5 HOH A 14 514 101 HOH HOH . F 5 HOH A 15 515 46 HOH HOH . F 5 HOH A 16 516 20 HOH HOH . F 5 HOH A 17 517 53 HOH HOH . F 5 HOH A 18 518 29 HOH HOH . F 5 HOH A 19 519 31 HOH HOH . F 5 HOH A 20 520 112 HOH HOH . F 5 HOH A 21 521 3 HOH HOH . F 5 HOH A 22 522 5 HOH HOH . F 5 HOH A 23 523 15 HOH HOH . F 5 HOH A 24 524 80 HOH HOH . F 5 HOH A 25 525 60 HOH HOH . F 5 HOH A 26 526 42 HOH HOH . F 5 HOH A 27 527 12 HOH HOH . F 5 HOH A 28 528 4 HOH HOH . F 5 HOH A 29 529 32 HOH HOH . F 5 HOH A 30 530 44 HOH HOH . F 5 HOH A 31 531 83 HOH HOH . F 5 HOH A 32 532 45 HOH HOH . F 5 HOH A 33 533 97 HOH HOH . F 5 HOH A 34 534 36 HOH HOH . F 5 HOH A 35 535 95 HOH HOH . F 5 HOH A 36 536 114 HOH HOH . F 5 HOH A 37 537 2 HOH HOH . F 5 HOH A 38 538 56 HOH HOH . F 5 HOH A 39 539 48 HOH HOH . F 5 HOH A 40 540 98 HOH HOH . F 5 HOH A 41 541 10 HOH HOH . F 5 HOH A 42 542 1 HOH HOH . F 5 HOH A 43 543 122 HOH HOH . F 5 HOH A 44 544 27 HOH HOH . F 5 HOH A 45 545 11 HOH HOH . F 5 HOH A 46 546 14 HOH HOH . F 5 HOH A 47 547 100 HOH HOH . F 5 HOH A 48 548 89 HOH HOH . F 5 HOH A 49 549 99 HOH HOH . F 5 HOH A 50 550 7 HOH HOH . F 5 HOH A 51 551 43 HOH HOH . F 5 HOH A 52 552 81 HOH HOH . F 5 HOH A 53 553 34 HOH HOH . F 5 HOH A 54 554 65 HOH HOH . F 5 HOH A 55 555 76 HOH HOH . F 5 HOH A 56 556 38 HOH HOH . F 5 HOH A 57 557 22 HOH HOH . F 5 HOH A 58 558 54 HOH HOH . F 5 HOH A 59 559 110 HOH HOH . F 5 HOH A 60 560 91 HOH HOH . F 5 HOH A 61 561 8 HOH HOH . F 5 HOH A 62 562 19 HOH HOH . F 5 HOH A 63 563 104 HOH HOH . F 5 HOH A 64 564 41 HOH HOH . F 5 HOH A 65 565 49 HOH HOH . F 5 HOH A 66 566 103 HOH HOH . F 5 HOH A 67 567 51 HOH HOH . F 5 HOH A 68 568 74 HOH HOH . F 5 HOH A 69 569 88 HOH HOH . F 5 HOH A 70 570 47 HOH HOH . F 5 HOH A 71 571 39 HOH HOH . F 5 HOH A 72 572 70 HOH HOH . F 5 HOH A 73 573 35 HOH HOH . F 5 HOH A 74 574 26 HOH HOH . F 5 HOH A 75 575 9 HOH HOH . F 5 HOH A 76 576 79 HOH HOH . F 5 HOH A 77 577 75 HOH HOH . F 5 HOH A 78 578 62 HOH HOH . F 5 HOH A 79 579 52 HOH HOH . F 5 HOH A 80 580 23 HOH HOH . F 5 HOH A 81 581 50 HOH HOH . F 5 HOH A 82 582 55 HOH HOH . F 5 HOH A 83 583 102 HOH HOH . F 5 HOH A 84 584 124 HOH HOH . F 5 HOH A 85 585 119 HOH HOH . F 5 HOH A 86 586 6 HOH HOH . F 5 HOH A 87 587 61 HOH HOH . F 5 HOH A 88 588 16 HOH HOH . F 5 HOH A 89 589 77 HOH HOH . F 5 HOH A 90 590 126 HOH HOH . F 5 HOH A 91 591 24 HOH HOH . F 5 HOH A 92 592 123 HOH HOH . F 5 HOH A 93 593 21 HOH HOH . F 5 HOH A 94 594 64 HOH HOH . F 5 HOH A 95 595 28 HOH HOH . F 5 HOH A 96 596 113 HOH HOH . F 5 HOH A 97 597 37 HOH HOH . F 5 HOH A 98 598 69 HOH HOH . F 5 HOH A 99 599 78 HOH HOH . F 5 HOH A 100 600 125 HOH HOH . F 5 HOH A 101 601 30 HOH HOH . F 5 HOH A 102 602 108 HOH HOH . F 5 HOH A 103 603 68 HOH HOH . F 5 HOH A 104 604 92 HOH HOH . F 5 HOH A 105 605 58 HOH HOH . F 5 HOH A 106 606 118 HOH HOH . F 5 HOH A 107 607 106 HOH HOH . F 5 HOH A 108 608 72 HOH HOH . F 5 HOH A 109 609 109 HOH HOH . F 5 HOH A 110 610 73 HOH HOH . F 5 HOH A 111 611 84 HOH HOH . F 5 HOH A 112 612 111 HOH HOH . F 5 HOH A 113 613 71 HOH HOH . F 5 HOH A 114 614 87 HOH HOH . F 5 HOH A 115 615 86 HOH HOH . F 5 HOH A 116 616 115 HOH HOH . F 5 HOH A 117 617 96 HOH HOH . F 5 HOH A 118 618 57 HOH HOH . F 5 HOH A 119 619 121 HOH HOH . F 5 HOH A 120 620 90 HOH HOH . F 5 HOH A 121 621 94 HOH HOH . F 5 HOH A 122 622 25 HOH HOH . F 5 HOH A 123 623 67 HOH HOH . F 5 HOH A 124 624 33 HOH HOH . F 5 HOH A 125 625 105 HOH HOH . F 5 HOH A 126 626 93 HOH HOH . F 5 HOH A 127 627 117 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 BR BR 6J7 . . . B 2 -6.054 -4.608 -10.916 0.23 16.68 ? BR 6J7 401 A 1 HETATM 2 C C9 6J7 . . . B 2 -6.234 -5.67 -12.526 1 20.63 ? C9 6J7 401 A 1 HETATM 3 N N4 6J7 . . . B 2 -5.713 -6.889 -12.575 1 19.99 ? N4 6J7 401 A 1 HETATM 4 C C8 6J7 . . . B 2 -6.04 -7.261 -13.82 1 17.16 ? C8 6J7 401 A 1 HETATM 5 C C7 6J7 . . . B 2 -5.801 -8.456 -14.621 1 21.01 ? C7 6J7 401 A 1 HETATM 6 O O6 6J7 . . . B 2 -5.175 -9.414 -14.112 1 23.9 ? O6 6J7 401 A 1 HETATM 7 N N3 6J7 . . . B 2 -6.277 -8.487 -15.86 1 18.79 ? N3 6J7 401 A 1 HETATM 8 C C6 6J7 . . . B 2 -6.958 -7.45 -16.4 1 18.66 ? C6 6J7 401 A 1 HETATM 9 N N2 6J7 . . . B 2 -7.401 -7.581 -17.661 1 20.72 ? N2 6J7 401 A 1 HETATM 10 N N1 6J7 . . . B 2 -7.213 -6.296 -15.739 1 15.87 ? N1 6J7 401 A 1 HETATM 11 C C5 6J7 . . . B 2 -6.791 -6.156 -14.471 1 14.01 ? C5 6J7 401 A 1 HETATM 12 N N 6J7 . . . B 2 -6.866 -5.19 -13.586 1 16.3 ? N 6J7 401 A 1 HETATM 13 C C4 6J7 . . . B 2 -7.526 -3.871 -13.717 1 14.29 ? C4 6J7 401 A 1 HETATM 14 C C2 6J7 . . . B 2 -7.007 -3.068 -14.908 1 12.61 ? C2 6J7 401 A 1 HETATM 15 O O4 6J7 . . . B 2 -6.641 -1.766 -14.424 1 12.37 ? O4 6J7 401 A 1 HETATM 16 O O5 6J7 . . . B 2 -8.945 -4.057 -13.863 1 14.63 ? O5 6J7 401 A 1 HETATM 17 C C3 6J7 . . . B 2 -9.333 -2.999 -14.756 1 11.16 ? C3 6J7 401 A 1 HETATM 18 C C 6J7 . . . B 2 -10.71 -3.151 -15.385 1 11.88 ? C 6J7 401 A 1 HETATM 19 O O1 6J7 . . . B 2 -10.848 -2.043 -16.281 1 11.72 ? O1 6J7 401 A 1 HETATM 20 C C1 6J7 . . . B 2 -8.236 -2.98 -15.801 1 10.61 ? C1 6J7 401 A 1 HETATM 21 O O3 6J7 . . . B 2 -8.333 -1.855 -16.684 1 12.14 ? O3 6J7 401 A 1 HETATM 22 P P 6J7 . . . B 2 -9.764 -1.821 -17.429 1 13.76 ? P 6J7 401 A 1 HETATM 23 O O 6J7 . . . B 2 -9.829 -3.013 -18.344 1 12.82 ? O 6J7 401 A 1 HETATM 24 O O2 6J7 . . . B 2 -9.958 -0.454 -18.013 1 12.29 ? O2 6J7 401 A 1 HETATM 25 H H10 6J7 . . . B 2 -6.112 -9.329 -16.392 1 22.55 ? H10 6J7 401 A 1 HETATM 26 H H8 6J7 . . . B 2 -7.223 -8.43 -18.177 1 24.86 ? H8 6J7 401 A 1 HETATM 27 H H9 6J7 . . . B 2 -7.9 -6.839 -18.083 1 24.86 ? H9 6J7 401 A 1 HETATM 28 H H7 6J7 . . . B 2 -7.345 -3.269 -12.82 1 17.15 ? H7 6J7 401 A 1 HETATM 29 H H3 6J7 . . . B 2 -6.177 -3.582 -15.411 1 15.13 ? H3 6J7 401 A 1 HETATM 30 H HO4 6J7 . . . B 2 -6.659 -1.176 -15.185 1 14.84 ? HO4 6J7 401 A 1 HETATM 31 H H6 6J7 . . . B 2 -9.308 -2.041 -14.217 1 13.39 ? H6 6J7 401 A 1 HETATM 32 H H1 6J7 . . . B 2 -10.781 -4.095 -15.929 1 14.26 ? H1 6J7 401 A 1 HETATM 33 H H 6J7 . . . B 2 -11.487 -3.123 -14.618 1 14.26 ? H 6J7 401 A 1 HETATM 34 H H5 6J7 . . . B 2 -8.291 -3.908 -16.393 1 12.73 ? H5 6J7 401 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 34 #